Python

Analyzing public GEO datasets with Pathomx

This short demo shows analysis of a publicly available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release). You can download the example dataset from here. Pathomx is an open-source workflow-based scientific analysis application. Source code is available here with packaged

Python

Pathomx: Example Analysis

Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service. The video shows an example analysis from processed data through to metabolic

Releases

Pathomx

Speed up your analysis with interactive data workflows built on Python.

Releases

Icoshift

A Python implementation of the icoshift spectral alignment algorithm.

Tutorials

Cytoscape v3.0.2 on Mac OS X

Cytoscape 3.0.2 was released on 1st August, a bugfix release for the 3.x series. However, there is a compatibility issue with the latest Java update from Apple resulting in Cytoscape hanging on startup. I'd followed advice found elsewhere to update to the latest Java version

Releases

accuri2fcs

Convert Accuri .c6 flow cytometry files to .fcs

Releases

gpml2svg

A command-line SVG renderer for GPML pathways

Python

cx_Freeze and PySide on Mac

I'd had success using py2app for building Mac binaries for distribution but wanted to give cx_Freeze a go since it's cross platform - allowing builds for Windows, Linux, and more. Unfortunately, attempting to build using cx_Freeze was resulting in errors: libpyside-python2.7.1.1.

Web Hosting

Pelicans on Webfaction

As mentioned in the previous post, I recently migrated this site over to the very clever Pelican. Setting it up was relatively straightforward using a combination of the official docs, this post and linked github repo from Dominic Rodger. That said, there were a few things that I stumbled at

Tutorials

Speed up MATLAB on MacOS X

On MacOS X 10.5 there is considerable slow-down in the MATLAB editor and other GUI elements. The issue is related to a change in the default Mac Java 2D rendering engine from Quartz2D (10.4) and Sun2D (10.5). This newer rendering engine improves performance for figure drawing, but

Tutorials

Customize directory colors

You can use the command ls --color (or an alias) to show directories with colours for folders, files, links, etc. However, you may not realise these colours can be easily configured using bashrc and a configuration file. Edit your .bashrc file (in your home directory) to include the following line:

Tutorials

Control memcached from the command line

memcached is a general-purpose distributed memory caching system originally developed by Danga Interactive for LiveJournal but now used by many other sites. It is often used to speed up dynamic database-driven websites by caching data and objects in RAM to reduce the number of times an external data source (such

Tutorials

Installing Haiku under Mac OS X with Virtualbox

Haiku is an open source operating system currently in development that specifically targets personal computing. Inspired by the Be Operating System, development began in 2001, and the operating system became self-hosting in 2008 with the first alpha release in September 2009, the second in May 2010 and the third in

Bash

Find all files containing a given string

A quick one-liner to recursively search files for a given text string. Open up a terminal session and enter the following - replacing "foo" with the text to search for. find . -exec grep -l "foo" {} \; You can also limit the search to files with a particular

Django

Django AJAX threaded-comments using jQuery

Upgrade threaded comments using mptt to allow AJAX submission of comments and update the template - without any backend hacking of Django. Everything is accomplished via Javascript and template tags. First set up Django threaded comments using mptt as described previously. First open up your comment form template form.html

Tutorials

Display external RSS feeds on your WordPress blog

Show another of your blogs or any other RSS news feed on your WordPress blog with this simple template code. Open your template file in either the WordPress admin editor or via FTP/SSH access to your hosting server. If you want to put the feed links in your sidebar

Tutorials

Highlight author's comments on WordPress blog

In this short tutorial we'll take a look at a simple trick to make comments from the original post author stand out a bit more in the comment listing – useful for seeing replies to comments. First you need to create a style to apply to highlighted comments on

Linux

Kill unresponsive applications on Linux

Sometimes things go a bit wrong. Sometimes they go very wrong. XKill is a simple little application that allows you to kill a running X application that has got out of kilter. Think of this as a quick way to get back control of your Desktop. xkill is installed by

Tutorials

Change the Desktop directory on Linux

On desktop setups where icons are shown on the desktop these are normally taken from the specific folder ~/Desktop. If you find you want to show icons from either your Home or another directory for a particular install/user you can do so by editing the user-dirs config file as

Linux

Collaborate in the shell with screen (multiuser)

Screen is a neat little program that allows you to use multiple virtual terminals in a single session on Unix/Linux and Mac. However, it does more than just that. It can also allow you to share your current session on a machine with another user - allowing you to

Tutorials

Installing Google Earth on Ubuntu

Install the latest version of Google Earth for Ubuntu Linux direct from Google sources. Open a terminal window to perform the installation (Ctrl-Alt-T) then enter the following at the prompt: wget http://dl.google.com/dl/earth/client/current/google-earth-stable_current_i386.deb For 64bit architecture use the following &

Tutorials

Syntax highlighting with Django and Markdown

Syntax highlighting is more than just eye candy. It can turn a block of impenetrable code into something more readable. To boost the usability of our code guides on this site we wanted to implement nice clear syntax highlighting of our hacks. Code samples are already marked up with markdown

Tutorials

Django Threaded Comments

Django ships with it's own comments contrib app that provides commenting on arbitrary models. However this is a flat-comment system which doesn't allow replying to comments. An app called django-threadedcomments exists but has not been updated for a number of versions and is broken. Other alternatives

Tutorials

Bash Command Substitution

Bash command substitution performs a given command replacing the marker with the resulting standard output. It is particularly useful when you want to store the output of a command in a variable or as an alternative method of chaining multiple commands together. Bash command substitution is achieved by wrapping your

Tutorials

Remove duplicate lines from text files (with sort)

A quick method to remove duplicates from text files - including for example CSV files - where multiple records have been added (perhaps automatically) at different times resulting in multiple copies of the same record scattered throughout the file. Here is a simple one-liner bash command to remove duplicates using